Subtle mitochondrial mutations as tumor markers

ABSTRACT

The accumulation of homoplasmic somatic mutations has been observed in the mitochondrial DNA of certain tumor cells. The presence or recurrence of a tumor can be detected by determining the presence of single basepair mutations in the mitochondrial genome from a cell sample of a patient.

This application claims the priority of provisional U.S. Application Ser. No. 60/097,307, filed Aug. 20, 1998, and is a continuation of U.S. application Ser. No. 09/377,856, filed Aug. 20, 1999 now U.S. Pat. No. 6,344,322.

The U.S. Government retains certain rights in this invention due to funding as provided by grant CA43460 awarded by the National Institutes of Health.

TECHNICAL FIELD OF THE INVENTION

The invention is related to the area of cancer genetics. In particular it is related to somatic mutations associated with cancer.

BACKGROUND OF THE INVENTION

The human mitochondrial genome is a 16 kilobase circular, double stranded DNA that encodes 13 polypeptides of the mitochondrial respiratory chain, 22 transfer RNAs, and two ribosomal RNAs required for protein synthesis. The mitochondrial genome is particularly susceptible to mutations because of the high level of reactive oxygen species generated in the organelle coupled with a low level of DNA repair (7-10). Surprisingly, there has been little detailed analysis of alterations in human mitochondrial DNA in cancer, although there are indications that mitochondria may be involved in neoplasia and apoptosis (2-6) as well as cancerous growth (1). Thus, there remains a need in the art to identify a correlation of alterations in human mitochondrial DNA with cancer.

SUMMARY OF THE INVENTION

It is an object of the invention to provide a method to aid in detecting the presence of tumor cells in a patient. This and other objects of the invention are provided by one or more of the embodiments described below.

One embodiment of the invention provides a method of screening patients for the presence of tumor cells. The method comprises a step for determining the presence of a single basepair mutation in a mitochondrial genome of a cell sample of a patient. If a single basepair substitution is found in a cell sample of the patient which is not in normal tissue of the patient, the patient is identified as having a tumor.

The invention thus provides the art with new methods of detecting and tracing tumors by examining mitochondrial DNA for the appearance of somatic mutations.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows examples of mitochondrial DNA mutations. The sequence of the mitochondrial genome was determined in normal cells, primary tumors, and tumor cell lines from the same patients. Arrows indicate the G-to-A transition (antisense strand) at codon 121 of the COX subunit I gene in line V425, an A insertion within the (A)8 tract of the ND5 gene in line V425, a T-to-C transition at codon 1 of the NDI gene in line 478, and a G-to-A transition (antisense strand) at codon 142 of the COX subunit II gene in line V429.

FIG. 2A to FIG. 2C depict somatic cell fusions. FIG. 2A. Confirmation of successful nuclear fusion using nuclear genomic DNA polymorphisms from the indicated lines. FIG. 2B. Analysis of the mitochondrial DNA utilizing the T-to-C variant at nucleotide 4,216 that creates a recognition site for Nla III (CATG). The C variant, giving rise to 376 and 231 fragments following restriction digest of a 1,140 bp PCR product, is present only in DLD-1 cells. FIG. 2C. Time course over which replicative advantage of DLD-1 mitochondria is evident. Initially, HCT 116 cell mitochondria were slightly over represented in the fusions, but a shift towards DLD-1 mitochondria was evident within five days and this process was complete between 15 and 60 days. DNA was isolated and the mitochondria were analyzed by Nla III digestion on the indicated days after cell fusion.

DETAILED DESCRIPTION OF THE INVENTION

The inventors have found that the presence of subtle mutations in the mitochondrial genome can be used as a means to trace the presence, spread, metastasis, growth, or recurrence of a tumor in a patient. Such subtle mutations include single basepair substitutions, single basepair insertions, and single basepair deletions. Single basepair substitutions can be either transitions or transversions, although the former are more frequent. Detection of such mutations can be useful to screen for the initial appearance of a tumor as well as the recurrence of a previously identified tumor. The methods are particularly suited to monitor anti-cancer therapy, recurrence, metastasis, and completeness of surgical removals.

A single basepair substitution is the substitution of a single nucleotide base with a different nucleotide base at the same position, with the corresponding substitution of the complementary base on the other strand of the DNA. While any single basepair substitution is conceivable within the scope of the invention, the most frequently encountered substitutions are those which are consistent with oxidative damage, such as T to C or G to A transitions. The mutations can appear in protein coding regions or in regions which encode ribosomal or transfer RNAs.

The homoplasmic property of most mutant mitochondrial genomes from tumors permits the ready detection of such mutations within a sample of mitochondrial DNA from a patient. Homoplasmic mutations are those which appear in essentially all of the copies of the mitochondrial genome within a given cell or tissue. However, heteroplasmic mutations, which are those appearing in only a fraction of the mitochondrial genomes of a cell or tissue, are also suitable for use with the invention.

Any cell sample can be tested from a patient who has cancer or is suspected of having cancer. Suitable cell samples include, but are not limited to, tissue from a growth suspected or known to be cancerous, tissue adjacent to a resection of a tumor, and tissue distant from the site of a tumor, such as lymph nodes which are suspected of bearing metastatic cells. Cells can also be obtained from bodily fluids or secretions, e.g., blood, urine, sputum, saliva, or feces, which may contain cancerous cells or metastatic cells. Cell samples can also be collected from other bodily secretions and tissues as is known in the art. A cell sample can be collected from suspected or known cancerous tissue or from bodily fluids or secretions harboring cancer cells as well as from suspected or known normal tissue or bodily fluids or secretions harboring normal cells.

In order to detect mutations of the mitochondrial genome from a cell sample of a patient, mitochondrial DNA can be isolated from the cell sample using any method known in the art. One way of identifying subtle mutations involves sequencing the mitochondrial DNA. This can be done according to any method known in the art. For example, isolated mitochondrial DNA can be cleaved using endonucleases into overlapping fragments of appropriate size for sequencing, e.g., about 1-3 kilobases in length, followed by polymerase chain reaction ICR) amplification and sequencing of the fragments. Examples of DNA sequencing methods are found in Brumley, R. L. Jr., and Smith, L. M., 1991, Rapid DNA sequencing by horizontal ultrathin gel electrophoresis, Nucleic Acids Res. 19:4121-4126 and Luckey, J. A., Drossman, H., Kostihka, T.; and Smith, L. M., 1993, High-speed DNA sequencing by capillary gel electrophoresis, Methods Enzymol. 218:154-172. Amplification methods such as PCR can be applied to samples as small as a single cell and still yield sufficient DNA for complete sequence analysis. The combined use of PCR and sequencing of mitochondrial DNA is described in Hopgood, R., Sullivan, K. M., and Gill, P., 1992, Strategies for automated sequencing of human mitochondrial DNA directly from PCR products, Biotechniques 13:82-92 and Tanaka, M., Hayakawa, M., and Ozawa, T., 1996, Automated sequencing of mitochondrial DNA, Methods Enzymol. 264:407-21.

Mutations can first be identified by comparison to sequences present in public databases for human mitochondrial DNA, e.g., at the URL address: http file type, www host server, gen.emory.edu domain name, mitomap.html directory. Any single basepair substitution identified in the sample DNA compared to a normal sequence from a database can be confirmed as being a somatic mutation as opposed to a polymorphic variant by comparing the sample mitochondrial DNA or sequences obtained from it to control cell mitochondrial DNA from the same individual or sequences obtained from it. Control cells are isolated from other apparently normal tissues, i.e., tissues which are phenotypically normal and devoid of any visible, histological, or immunological characteristics of cancer tissue. A difference between the sample and the control identifies a somatic mutation which is associated with the tumor.

An alternative to serially sequencing the entire mitochondrial genome in order to identify a single basepair substitution is to use hybridization of the mitochondrial DNA to an array of oligonucleotides. Hybridization techniques are available in the art which can rapidly identify mutations by comparing the hybridization of the sample to matched and mismatched sequences which are based on the human mitochondrial genome. Such an array can be as simple as two oligonucleotide probes, one of whose sequence matches the wild-type or mutant region containing the single base substitution (matched probe) and another whose sequence includes a single mismatched base (mismatch control probe). If the sample DNA hybridizes to the matched probe but not the mismatched probe, it is identified as having the same sequence as the matched probe. Larger arrays containing thousands of such matched/mismatched pairs of probes on a glass slide or microchip (“microarrays” or “gene chips”) are available which are capable of sequencing the entire mitochondrial genome very quickly. Such arrays are commercially available. Review articles describing the use of microarrays in genome and DNA sequence analysis and links to their commercial suppliers are available at the URL address: www host server, gene-chips.com domain name.

The invention can be used to screen patients suspected of having cancer for the presence of tumor cells. A cell sample is first obtained from a suspected tumor of the patient, or is obtained from another source such as blood or lymph tissue, for example, if metastasis is suspected. The cell sample is tested to determine the presence of a single basepair mutation in mitochondrial DNA from the cell sample using the techniques outlined above. Optionally, a cell sample from normal, non-cancerous cells or tissue of the patient is also obtained and is tested for the presence or absence of a single basepair mutation in mitochondrial DNA. If a single basepair mutation is determined which is not present in a cell sample from normal tissue of the patient, then the mutation is a somatic mutation and the presence of tumor cells in the patient is indicated. If one or more single basepair mutations are determined in the mitochondrial genome of the cell sample of the patient, then the patient is identified as having a tumor. As in any diagnostic technique for cancer, to confirm or extend the diagnosis, further diagnostic techniques may be warranted. For example, conventional histological examination of a biopsy specimen can be performed to detect the presence of tumor cells, or analysis of a tumor-specific antigen in a blood or tissue sample can be performed.

The method outlined above can be practiced either in the situation where the somatic mutation is previously known or previously unknown. Based on the inventors' findings, the identification of a previously unknown somatic mutation in a mitochondrial genome of a cell of a patient is likely to indicate the presence of tumor cells in the patient. Therefore, the method can be practiced even in the absence of prior knowledge about any particular somatic mutation. The method can also be carried out subsequent to the discovery of a somatic mutation in a mitochondrial genome of a cell of the patient or of another patient. In this case, a previous association of the somatic mutation with the presence of a tumor in the patient or in another patient strongly indicates the presence of tumor cells in the patient. It may also indicate the recurrence of a tumor or the incomplete prior removal of cancerous tissue from the patient.

The effectiveness of therapy can be evaluated when a tumor has already been identified and found to contain a single basepair substitution in the mitochondrial genome. Once a single basepair mutation has been identified in the mitochondrial DNA of a tumor of the patient, further tumor cells can be detected in tissue surrounding a resection or at other sites, if metastasis has occurred. Using the methods outlined above, the recurrence of the tumor or its incomplete removal can be assessed. Similarly, if a tumor has been treated using a non-surgical method such as chemotherapy or radiation, then the success of the therapy can be evaluated at later times by repeating the analysis. The step for determining the presence of a single basepair mutation in a mitochondrial genome of a cell sample of a patient can be performed 1, 2, 3, 4, 5, 6, 8, 10, or more times in order to monitor the development or regression of a tumor or to monitor the progress or lack of progress of therapy undertaken to eliminate the tumor.

Upon repeated analyses, the step for determining the presence of a single basepair mutation is simplified, because only a well defined and limited region of the genome need be sequenced. Using the hybridization method, for example, it is possible to evaluate the presence of the mutation with only a single matched/mismatched pair of oligonucleotide probes in the array. In the event that a mixture of genotypes is observed, it is possible to obtain quantitative information about the relative amount of each mitochondrial genotype using techniques known to the art, e.g., hybridization. Quantitative analysis can reveal changes in the relative proportion of tumor to normal cells in a tissue over time or in response to therapy.

The methods described above were used to study somatic mutations in mitochondrial DNA from human colorectal tumor cells (see Examples 1 and 2). The mutations observed generally were transitions, affecting G residues, which are the preferred targets for oxidative damage to DNA in general and mitochondrial DNA in particular (at least in vitro) (12, 13, 17, 18). This mutational spectrum supports the idea that the mitochondrial DNA mutations resulted from the reactive oxygen species continually generated in mitochondria. Sequence analyses of nuclear genes from the same ten cell lines studied for mitochondrial DNA mutations indicated that the prevalence of mutations is at least ten-fold higher in the mitochondrial genome than in the nuclear genome of those cells. Previous experiments have demonstrated large deletions in the mitochondrial DNA of some tumors (19-23), rather than the subtle mutations observed here. No deletions were observed in the cell lines studied here, despite several attempts to find them using multiple primer pairs in PCR-based strategies. The literature reveals no previous attempts to search for subtle mutations of mitochondrial genomes by complete sequencing.

The mutations reported in Table 1 were mostly homoplasmic, while the deletions previously observed in tumor cells or normal cells of aging individuals were generally heteroplasmic, present only in a small proportion of the mitochondrial population (19-24). The results presented here are not at variance with a previous study in which no somatic mutations in 200 bp of D-loop sequence were found. This D loop sequence contains promotor elements for transcription of the mitochondrial genome, while the mutations discovered by the inventors were confined to regions encoding mitochondrial proteins or rRNA.

The striking and unexpected homoplasmy of the mutations identified by the inventors indicates significant selection at several levels. First, the somatically mutant mitochondrial genome must be replicated better than that present in the germ-line. Previous experiments have indicated that replication of mitochondria can be controlled individually, in that signals from aberrantly functioning mitochondria induce their overreplication, perhaps in a compensating effort (25). The fusion experiments of Example 2 demonstrate that the process of mitochondrial selection in tumor cells can take place rapidly (FIG. 2C). Over the thousands of generations required for tumorigenesis in vivo, this process could easily result in the replacement of all mitochondrial genomes within the cell with a mutant form. This cell could then overtake the population through clonal growth, either because the aberrant mitochondria themselves endowed the cell with a selective growth advantage or because that cell sustained a nuclear gene mutation providing such an advantage.

This explanation invokes the idea that the mitochondrial mutations may themselves have a functional effect. It is unlikely that most of the observed somatic mutations result in major perturbations of mitochondrial function, as oxygen consumption and the respiratory chain enzymatic activities of several of the lines listed in Table 1 were largely normal. Instead, these mutations, perhaps in concert with polymorphic variations in mitochondrial DNA, probably result in subtle changes which might generate slightly higher levels of ROS. It has been shown that low levels of ROS are highly mitogenic, while high ROS levels are toxic (9). Regardless of the mechanism for their selection, however, the mutations that have been identified represent a previously unrecognized alteration in tumor cells that could have significant effects on the cellular processes controlled by mitochondria. Their homoplasmy raises fascinating questions about the control of mitochondrial DNA at the intramitochondrial, intracellular, and cellular population levels. It indicatea that a single cell with a mutant mitochondrial genome had acquired a selective growth advantage during tumor evolution, allowing it to become the predominant cell type within the tumor cell population. Furthermore, it is important to appreciate that cells, including the colorectal cancer cell lines used here, each contain hundreds of mitochondria, and each mitochondrion contains one to ten DNA molecules (14). The homoplasmy therefore additionally indicates that each mutant mitochondrial genome had a replicative advantage within the particular mitochondrion in which it occurred, and that this mitochondrion had selectively proliferated over other mitochondria in the same cell. Alterations of tumor mitochondrial DNA may also provide clues to their environmental or genetic background, a hypothesis that can be tested in the future using DNA chip technologies (26).

The above disclosure generally describes the present invention. A more complete understanding can be obtained by reference to the following specific examples, which are provided herein for purposes of illustration only and are not intended to limit the scope of the invention.

EXAMPLE 1 Identification of Somatic Mutations in Mitochondrial DNA of Human Colorectal Cancer Cells

To determine whether mutations of the mitochondrial DNA were present in human colorectal tumors, the entire mitochondrial genome was PCR-amplified from ten human colorectal cancer cell lines in 1-3 kb overlapping fragments and the PCR products completely sequenced. The use of large PCR products excluded the possibility that nuclear pseudogenes would complicate this analysis (11).

Cell Lines and Tumors Derivation and maintenance of the VACO lines has been previously described (27). The DLD-1, HCT116, SW837 and HT29 human colorectal cancer cell lines were obtained from ATCC and maintained in McCoy's medium (Gibco, BRL) supplemented with 10% fetal bovine serum (Hyclone) and antibiotics (Gibco, BRL).

DNA Purification, PCR Amplification and Sequencing Cellular DNA from cell lines, from primary tumors, and from normal colonic mucosa was isolated as previously described (28). Overlapping fragments (1-3 kb each) of the mitochondrial genome were amplified by PCR using this DNA as template. The sequencing method allowed the detection of any mutation present in >25% of the mitochondrial DNA molecules within a given sample. In selected cases, the validity of the sequence data was confirmed using purified mitochondrial DNA as templates. To confirm the mutations in the primary tumors, smaller PCR fragments were generated from the DNA purified from microdissected, paraffin-embedded samples. Manual sequencing of the DNA fragments was performed using Thermosequenase (Amersham) and a Genomyx electrophoresis apparatus (Beckman).

Sequence analysis. The sequences obtained were first compared to those recorded in the mitochondrial databank at www.gen.emory.edu/mitomap.html the URL address: www host server, gen.emory.edu domain name, mitomap.html directory. Eighty-eight sequence variants were identified (4-31 per tumor) that were not recorded in this databank. These included 27 variants which were predicted to alter the amino acid sequence of the encoded protein, 48 variants which were in protein coding regions but predicted to be silent, and 13 which affected rRNA or tRNA genes.

The database search provided only preliminary evidence for mutations, however, as it could not distinguish somatic mutations from rare germ-line variants. To make this distinction, mitochondrial DNA sequences were determined from normal colons from the same patient. This analysis showed that at least seven of the lines contained true somatic mutations. Three of the lines contained a single mutation, while four others contained two or three mutations (Table 1).

Each of the 27 sequence variants predicted to result in amino acid changes was evaluated to determine its somatic nature; of these, eight were found to be somatic and 19 were found in the germline of the same patient. Of the 13 variants in rRNA or tRNA genes, nine were evaluated in this way and four were found to be somatic. Twenty-five of the 48 silent mutations were also evaluated, and none of these were found to be somatic.

Of the 12 somatic mutations identified, eight were in protein encoding genes and four were in rRNA genes (Table 1). Eleven were nucleotide substitutions and one was a single bp insertion. Of the eight mutations in protein-encoding genes, one was a nonsense mutation, one was a 1-bp insertion, and six were missense mutations (Table 1). All but one of the 11 nt substitutions were T to C or G to A transitions. This mutational spectrum is fully consistent with the known mutagenic spectra of oxidative damage (12, 13).

To determine whether these mutations arose in vivo rather than during the process of cell culture, DNA was purified from five of the primary tumors from which the lines were derived (in two cases, no primary tumors were available). In every evaluable case, the mutation was found in the primary tumor as well as in the cell line (examples in FIG. 1).

Surprisingly, each of the 12 mutations was present in a major portion of the mitochondrial DNA molecules, and in ten of the 12 cases, the mutations were homoplasmic, i.e., apparently present in every mitochondrial genome (Table 1). This homoplasmy was observed both in the primary tumors as well as in the cell lines (FIG. 1).

EXAMPLE 2 Proliferation of Mitochondria Harboring Somatic Mutations

Cell fusion experiments have indicated that mitochondria from tumor cells can selectively proliferate when such cells are fused to normal cells (15). The inventors sought to determine whether a similar mitochondrial dominance could be observed upon fusion between two colorectal cancer cell lines. Attempts to fuse the lines studied for mitochondrial mutations were unsuccessful for technical reasons. Therefore, more commonly used colorectal cancer cell lines were employed in which intercellular fusions are possible (16).

Geneticin-resistant DLD-1 cells were fused to hygromycin-resistant subclones of each of three different colorectal cancer cell lines CACTI 16, HT29, and SW837). Geneticin- or hygromycin-resistant clones were derived through transfection of appropriate plasmid vectors. Approximately 106 hygromycin-resistant cells were mixed with an equal number of neomycin-resistant cells and fused by PEG treatment as described (16). Hybrids were selected in standard growth medium containing 1 mg/ml geneticin and 0.25 mg/ml hygromycin (DLD-1-HCT116 fusion), 1.5 mg/ml geneticin and 0.6 mg/ml hygromycin (D)LD-HT29 fusion) and 1 mg/ml geneticin and 0.25 mg/ml hygromycin (DLD-SW837 fusion). Successful fusions were verified by nuclear genotyping. Allelotyping was carried out as described (29) using the primer pair wglg5 A/wglg5B or MapPair primers for D19S591 and D16S764 (Research Genetics). Amplified fragments were resolved by electrophoresis in 8% polyacrylamide gels. Reactions using radioactively labeled primers were separated on a 4.5% sequencing gel (Genomyx), while reactions using fluorescence labeled primers were analyzed on an ABI Sequencing System (Perkin-Elmer).

The success of fusion was demonstrated using nuclear genomic polymorphisms (FIG. 2A). Complete sequencing of the mitochondrial genomes revealed 3-7 potential variants in each line; it could not be determined which of these were somatic, as normal cells derived from the individuals from whom the cell lines were derived were not available. However, these variants provided a convenient method to trace the fate of the mitochondrial DNA in the fusions. In particular, a T to C variant at nucleotide 4,216 was used that creates a restriction endonuclease recognition site for Nla III (FIG. 2B). The C variant was present in DLD-1 cells but not in any of the other three lines. As shown in FIG. 2B, the DLD-1 mitochondria were “dominant” over the other mitochondria in each of the fusions. All three tested clones derived from DLD-IAHCT116 fusions contained mitochondria exclusively of DLD-1 origin. A pool of over 100 stable clones from this fusion also contained only mitochondria from DLD-lcells. DLD-1 mitochondria were also dominant to those from HT29 and SW837 cells, contributing either all or the majority of mitochondrial genomes in the clones tested (FIG. 2B).

To determine the time course over which the replicative advantage of DLDl-1 mitochondria occurred, pooled clones from DLD-1HCT116 fusions were followed. At the initiation of this experiment, there was a mixture of mitochondrial genomes, with a slight excess of the mitochondria from HCT116 cells. Within five days, a skewing towards DLD-1 mitochondria was evident, and a major shift occurred between 15 and 60 days after fusion, by which time only DLD-1 mitochondria remained in the hybrids (FIG. 2C). Whether it was strictly the mitochondria, or a combination of nuclear and mitochondrial factors, that was responsible for the selection of DLD-1 mitochondria could not be determined. However, these experiments clearly documented that tumor mitochondria of one type can have a significant replicative advantage over other types, and are consistent with other experiments documenting the potential for mitochondrial dominance (15).

REFERENCES

1. Warburg, O. On the origin of cancer cells. Science 123, 309-314 (1956).

2. Kroemer, G., Zamzami, N. & Susin, S. A. Mitochondrial control of apoptosis. Immun. Today 18, 45-51 (1997).

3. Korsmeyer, S. J., Yin, X. M., Oltvai, Z. N. Veis-Novack, D. J. & Linette, G. P. Reactive oxygen species and the regulation of cell death by the BcI-2 gene family. Biochim. Biophys. Acta 1271, 63-66 (1995).

4. Rudin, C. M. & Thompson, C. B. Apoptosis and disease: regulation and clinical relevance of programmed cell death. Annu. Rev. Med. 48, 267-281 (1997).

5. Wang, H. G. & Reed, J. C. Mechanisms of BcI-2 protein function. Histol. Histopathol. 13, 521-530 (1998).

6. Cavalli, L. R. & B. C., L. Mutagenesis, tumorigenicity, and apoptosis: are the mitochondria involved? Muta. Res. 398, 19-26 (1998).

7. Lightowlers R N, C. P., Turnbull D M, Howell N. Mammalian mitochondrial genetics: heredity, heteroplasmy and disease. Trends Genet. 13, 450-455 (1997).

8. Beal, M. Mitochondria, free radical, and neurodegeneration. Curr. Opin. Neurobiol. 6, 661-666 (1996).

9. Li, Y., Zhou, H., Stansbury, K. & Trush, M. Role of reactive oxygen species in multistage carcinogenesis. in Oxygen radicals ad the disease process (eds. Thomas, C. & Kalyanaraman, B.) 237-277 (Harwood Academic Publishers, 1997).

10. Croteau, D. L. & Bohr, V. A. Repair of oxidative damage to nuclear and mitochondrial DNA in mammalian cells. J. Biol. Chem. 272, 25409-25412 (1997).

11. Parfait B. R. P., Munnich A, Rotig A. Co-amplification of nuclear pseudogenes and assessment of heteroplasmy of mitochondrial DNA mutations. Biochem. Biophys. Res. Commun. 247, 57-59 (1998).

12. Beckman, K. B. & Ames, B. N. Oxidative decay of DNA. J. Biol. Chem. 272, 19633-6 (1997).

13. Cadet, J., Berger, M. Douki, T. & Ravanat, J. L. Oxidative damage to DNA: formation measurement, and biological significance. Rev. Physiol. Biochem. Pharmacol. 131, 1-87 (1997).

14. Wallace, D. C., Brown, M. D., Melov, S., Graham, B. & Lott, M. Mitochondrial biology degenerative diseases and aging. Biofactors 7, 187-190 (1998).

15. Shay, J. & Ishii, S. Unexpected nonrandom mitochondrial DNA segregation in human cell hybrids. Anticancer. Res. 10, 279-284 (1990).

16. Lengauer, C., Kinzler, K. W. & Vogelstein, B. Genetic instability in colorectal cancers. Nature 386, 623-627 (1997).

17. Khrapko, K. et al. Mitochondrial mutational spectra in human cells and tissues. Proc. Natl. Acad Sci. U.S.A. 94, 13798-13803 (1997).

18. Beckman, K. & Ames, B. Detection and guantification of oxidative adducts of mitochondrial DNA. Methods Enzymol. 264, 442-153 (1996).

19. Welter, C., Kovacs, G., Seitz, G. & Blin, N. Alteration of mitochondrial DNA in human oncocyomas. Genes Chromosomes Cancer 1, 79-82 (1989).

20. Yamamoto, H. et al. Significant existence of deleted mitochondrial DNA in cirrhotic liver surrounding hepatic tumor. Biochem. Biophys. Res. Commun. 182, 913-920 (1992).

21. Burgart, L. J. Zheng, J., Shu, Q., Strickler, J. G. & Shibata, D. Somatic mitochondrial mutation in gastric cancer. Am. J Pathol. 147, 1105-1111 (1995).

22. Tallini, G. Ladanyi, M., Roasi, J. & Thanwar, S. Analysis of nuclear and mitochondrial DNA alterations in thyroid and renal oncocytic tumour. Cytogenet. Cell Genet. 66, 253-259 (1994).

23. Heerdt, G. G., Chen, J., Stewart, L. R. & Augenlicht, L. H. Polymorphisms, but lack of mutations or instability, the promotor region of the mitochondrial genome in human colonic tumors. Cancer Res. 54, 3912-3915 (1994).

24. Wallace, D. C. Mitochondrial DNA sequence variation in human evolution and disease. Proc Natl. Acad. Sci. U.S.A. 91, 87-3946 (1994).

25. Attardi, g., Yoneda, M. & Chomyn, A. Complementation and segregation behavior of disease-causing mitochondrial DNA mutation in cellular model systems. Biochim. Biophys. Acta 1271, 241-248 (1995).

26. Chee, M. et al. Accessing genetic information with high-density DNA arrays. Science 274, 610-614 (1996).

27. Parsons, R. et al. Microsateffite instability and mutations of the transforming growth factor beta type 11 Receptor gene in colorectal cancer. Cancer Res. 55, 5548-5550 (1995).

28. Jen, J. et al. Allelic loss of chromosome 18q and prognosis in colorectal cancer. N. England. J. Med. 331, 213-221 (1994).

29. Armour, J. A., Neumann, R., Gobert, S. & Jeffreys, A. J. Isolation of human simple repeat loci by hybridization selection. Hum. Mol. Genet. 3, 599-565 (1994).

TABLE 1 Summary of mtDNA mutations Tumor* Position DNA Protein Gene V478 710 T→C — 12S rRNA ″ 1738 T→C — 16S rRNA ″ 3308 T→C M1T ND1 V429 8009 G→A V142M COX subunit II ″ 14985 G→A R80H CYT b ″ 15572 T→C F276L CYT b V441 9949 G→A V2481 COX subunit III V456 10563 T→C C32R ND4L V425 6264 G→A G121trun COX subunit I ″ 12418 insA K28frameshift ND5 V451 1967 T→C — 16S rRNA V410 2299 T→A — 16S rRNA *All the mutations were homoplasmic except V451 T11967C and V410 T2299A, which were present in ˜50% of the mitochondrial DNA molecules.

1 1 16569 DNA Homo sapiens 1 gatcacaggt ctatcaccct attaaccact cacgggagct ctccatgcat ttggtatttt 60 cgtctggggg gtatgcacgc gatagcattg cgagacgctg gagccggagc accctatgtc 120 gcagtatctg tctttgattc ctgcctcatc ctattattta tcgcacctac gttcaatatt 180 acaggcgaac atacttacta aagtgtgtta attaattaat gcttgtagga cataataata 240 acaattgaat gtctgcacag ccactttcca cacagacatc ataacaaaaa atttccacca 300 aaccccccct cccccgcttc tggccacagc acttaaacac atctctgcca aaccccaaaa 360 acaaagaacc ctaacaccag cctaaccaga tttcaaattt tatcttttgg cggtatgcac 420 ttttaacagt caccccccaa ctaacacatt attttcccct cccactccca tactactaat 480 ctcatcaata caacccccgc ccatcctacc cagcacacac acaccgctgc taaccccata 540 ccccgaacca accaaacccc aaagacaccc cccacagttt atgtagctta cctcctcaaa 600 gcaatacact gaaaatgttt agacgggctc acatcacccc ataaacaaat aggtttggtc 660 ctagcctttc tattagctct tagtaagatt acacatgcaa gcatccccgt tccagtgagt 720 tcaccctcta aatcaccacg atcaaaaggg acaagcatca agcacgcagc aatgcagctc 780 aaaacgctta gcctagccac acccccacgg gaaacagcag tgattaacct ttagcaataa 840 acgaaagttt aactaagcta tactaacccc agggttggtc aatttcgtgc cagccaccgc 900 ggtcacacga ttaacccaag tcaatagaag ccggcgtaaa gagtgtttta gatcaccccc 960 tccccaataa agctaaaact cacctgagtt gtaaaaaact ccagttgaca caaaatagac 1020 tacgaaagtg gctttaacat atctgaacac acaatagcta agacccaaac tgggattaga 1080 taccccacta tgcttagccc taaacctcaa cagttaaatc aacaaaactg ctcgccagaa 1140 cactacgagc cacagcttaa aactcaaagg acctggcggt gcttcatatc cctctagagg 1200 agcctgttct gtaatcgata aaccccgatc aacctcacca cctcttgctc agcctatata 1260 ccgccatctt cagcaaaccc tgatgaaggc tacaaagtaa gcgcaagtac ccacgtaaag 1320 acgttaggtc aaggtgtagc ccatgaggtg gcaagaaatg ggctacattt tctaccccag 1380 aaaactacga tagcccttat gaaacttaag ggtcgaaggt ggatttagca gtaaactaag 1440 agtagagtgc ttagttgaac agggccctga agcgcgtaca caccgcccgt caccctcctc 1500 aagtatactt caaaggacat ttaactaaaa cccctacgca tttatataga ggagacaagt 1560 cgtaacatgg taagtgtact ggaaagtgca cttggacgaa ccagagtgta gcttaacaca 1620 aagcacccaa cttacactta ggagatttca acttaacttg accgctctga gctaaaccta 1680 gccccaaacc cactccacct tactaccaga caaccttagc caaaccattt acccaaataa 1740 agtataggcg atagaaattg aaacctggcg caatagatat agtaccgcaa gggaaagatg 1800 aaaaattata accaagcata atatagcaag gactaacccc tataccttct gcataatgaa 1860 ttaactagaa ataactttgc aaggagagcc aaagctaaga cccccgaaac cagacgagct 1920 acctaagaac agctaaaaga gcacacccgt ctatgtagca aaatagtggg aagatttata 1980 ggtagaggcg acaaacctac cgagcctggt gatagctggt tgtccaagat agaatcttag 2040 ttcaacttta aatttgccca cagaaccctc taaatcccct tgtaaattta actgttagtc 2100 caaagaggaa cagctctttg gacactagga aaaaaccttg tagagagagt aaaaaattta 2160 acacccatag taggcctaaa agcagccacc aattaagaaa gcgttcaagc tcaacaccca 2220 ctacctaaaa aatcccaaac atataactga actcctcaca cccaattgga ccaatctatc 2280 accctataga agaactaatg ttagtataag taacatgaaa acattctcct ccgcataagc 2340 ctgcgtcaga ttaaaacact gaactgacaa ttaacagccc aatatctaca atcaaccaac 2400 aagtcattat taccctcact gtcaacccaa cacaggcatg ctcataagga aaggttaaaa 2460 aaagtaaaag gaactcggca aatcttaccc cgcctgttta ccaaaaacat cacctctagc 2520 atcaccagta ttagaggcac cgcctgccca gtgacacatg tttaacggcc gcggtaccct 2580 aaccgtgcaa aggtagcata atcacttgtt ccttaaatag ggacctgtat gaatggctcc 2640 acgagggttc agctgtctct tacttttaac cagtgaaatt gacctgcccg tgaagaggcg 2700 ggcataacac agcaagacga gaagacccta tggagcttta atttattaat gcaaacagta 2760 cctaacaaac ccacaggtcc taaactacca aacctgcatt aaaaatttcg gttggggcga 2820 cctcggagca gaacccaacc tccgagcagt acatgctaag acttcaccag tcaaagcgaa 2880 ctactatact caattgatcc aataacttga ccaacggaac aagttaccct agggataaca 2940 gcgcaatcct attctagagt ccatatcaac aatagggttt acgacctcga tgttggatca 3000 ggacatcccg atggtgcagc cgctattaaa ggttcgtttg ttcaacgatt aaagtcctac 3060 gtgatctgag ttcagaccgg agtaatccag gtcggtttct atctaccttc aaattcctcc 3120 ctgtacgaaa ggacaagaga aataaggcct acttcacaaa gcgccttccc ccgtaaatga 3180 tatcatctca acttagtatt atacccacac ccacccaaga acagggtttg ttaagatggc 3240 agagcccggt aatcgcataa aacttaaaac tttacagtca gaggttcaat tcctcttctt 3300 aacaacatac ccatggccaa cctcctactc ctcattgtac ccattctaat cgcaatggca 3360 ttcctaatgc ttaccgaacg aaaaattcta ggctatatac aactacgcaa aggccccaac 3420 gttgtaggcc cctacgggct actacaaccc ttcgctgacg ccataaaact cttcaccaaa 3480 gagcccctaa aacccgccac atctaccatc accctctaca tcaccgcccc gaccttagct 3540 ctcaccatcg ctcttctact atgaaccccc ctccccatac ccaaccccct ggtcaacctc 3600 aacctaggcc tcctatttat tctagccacc tctagcctag ccgtttactc aatcctctga 3660 tcagggtgag catcaaactc aaactacgcc ctgatcggcg cactgcgagc agtagcccaa 3720 acaatctcat atgaagtcac cctagccatc attctactat caacattact aataagtggc 3780 tcctttaacc tctccaccct tatcacaaca caagaacacc tctgattact cctgccatca 3840 tgacccttgg ccataatatg atttatctcc acactagcag agaccaaccg aacccccttc 3900 gaccttgccg aaggggagtc cgaactagtc tcaggcttca acatcgaata cgccgcaggc 3960 cccttcgccc tattcttcat agccgaatac acaaacatta ttataataaa caccctcacc 4020 actacaatct tcctaggaac aacatatgac gcactctccc ctgaactcta cacaacatat 4080 tttgtcacca agaccctact tctaacctcc ctgttcttat gaattcgaac agcatacccc 4140 cgattccgct acgaccaact catacacctc ctatgaaaaa acttcctacc actcacccta 4200 gcattactta tatgatatgt ctccataccc attacaatct ccagcattcc ccctcaaacc 4260 taagaaatat gtctgataaa agagttactt tgatagagta aataatagga gcttaaaccc 4320 ccttatttct aggactatga gaatcgaacc catccctgag aatccaaaat tctccgtgcc 4380 acctatcaca ccccatccta aagtaaggtc agctaaataa gctatcgggc ccataccccg 4440 aaaatgttgg ttataccctt cccgtactaa ttaatcccct ggcccaaccc gtcatctact 4500 ctaccatctt tgcaggcaca ctcatcacag cgctaagctc gcactgattt tttacctgag 4560 taggcctaga aataaacatg ctagctttta ttccagttct aaccaaaaaa ataaaccctc 4620 gttccacaga agctgccatc aagtatttcc tcacgcaagc aaccgcatcc ataatccttc 4680 taatagctat cctcttcaac aatatactct ccggacaatg aaccataacc aatactacca 4740 atcaatactc atcattaata atcataatag ctatagcaat aaaactagga atagccccct 4800 ttcacttctg agtcccagag gttacccaag gcacccctct gacatccggc ctgcttcttc 4860 tcacatgaca aaaactagcc cccatctcaa tcatatacca aatctctccc tcactaaacg 4920 taagccttct cctcactctc tcaatcttat ccatcatagc aggcagttga ggtggattaa 4980 accagaccca gctacgcaaa atcttagcat actcctcaat tacccacata ggatgaataa 5040 tagcagttct accgtacaac cctaacataa ccattcttaa tttaactatt tatattatcc 5100 taactactac cgcattccta ctactcaact taaactccag caccacgacc ctactactat 5160 ctcgcacctg aaacaagcta acatgactaa cacccttaat tccatccacc ctcctctccc 5220 taggaggcct gcccccgcta accggctttt tgcccaaatg ggccattatc gaagaattca 5280 caaaaaacaa tagcctcatc atccccacca tcatagccac catcaccctc cttaacctct 5340 acttctacct acgcctaatc tactccacct caatcacact actccccata tctaacaacg 5400 taaaaataaa atgacagttt gaacatacaa aacccacccc attcctcccc acactcatcg 5460 cccttaccac gctactccta cctatctccc cttttatact aataatctta tagaaattta 5520 ggttaaatac agaccaagag ccttcaaagc cctcagtaag ttgcaatact taatttctgt 5580 aacagctaag gactgcaaaa ccccactctg catcaactga acgcaaatca gccactttaa 5640 ttaagctaag cccttactag accaatggga cttaaaccca caaacactta gttaacagct 5700 aagcacccta atcaactggc ttcaatctac ttctcccgcc gccgggaaaa aaggcgggag 5760 aagccccggc aggtttgaag ctgcttcttc gaatttgcaa ttcaatatga aaatcacctc 5820 ggagctggta aaaagaggcc taacccctgt ctttagattt acagtccaat gcttcactca 5880 gccattttac ctcaccccca ctgatgttcg ccgaccgttg actattctct acaaaccaca 5940 aagacattgg aacactatac ctattattcg gcgcatgagc tggagtccta ggcacagctc 6000 taagcctcct tattcgagcc gagctgggcc agccaggcaa ccttctaggt aacgaccaca 6060 tctacaacgt tatcgtcaca gcccatgcat ttgtaataat cttcttcata gtaataccca 6120 tcataatcgg aggctttggc aactgactag ttcccctaat aatcggtgcc cccgatatgg 6180 cgtttccccg cataaacaac ataagcttct gactcttacc tccctctctc ctactcctgc 6240 tcgcatctgc tatagtggag gccggagcag gaacaggttg aacagtctac cctcccttag 6300 cagggaacta ctcccaccct ggagcctccg tagacctaac catcttctcc ttacacctag 6360 caggtgtctc ctctatctta ggggccatca atttcatcac aacaattatc aatataaaac 6420 cccctgccat aacccaatac caaacgcccc tcttcgtctg atccgtccta atcacagcag 6480 tcctacttct cctatctctc ccagtcctag ctgctggcat cactatacta ctaacagacc 6540 gcaacctcaa caccaccttc ttcgaccccg ccggaggagg agaccccatt ctataccaac 6600 acctattctg atttttcggt caccctgaag tttatattct tatcctacca ggcttcggaa 6660 taatctccca tattgtaact tactactccg gaaaaaaaga accatttgga tacataggta 6720 tggtctgagc tatgatatca attggcttcc tagggtttat cgtgtgagca caccatatat 6780 ttacagtagg aatagacgta gacacacgag catatttcac ctccgctacc ataatcatcg 6840 ctatccccac cggcgtcaaa gtatttagct gactcgccac actccacgga agcaatatga 6900 aatgatctgc tgcagtgctc tgagccctag gattcatctt tcttttcacc gtaggtggcc 6960 tgactggcat tgtattagca aactcatcac tagacatcgt actacacgac acgtactacg 7020 ttgtagccca cttccactat gtcctatcaa taggagctgt atttgccatc ataggaggct 7080 tcattcactg atttccccta ttctcaggct acaccctaga ccaaacctac gccaaaatcc 7140 atttcactat catattcatc ggcgtaaatc taactttctt cccacaacac tttctcggcc 7200 tatccggaat gccccgacgt tactcggact accccgatgc atacaccaca tgaaacatcc 7260 tatcatctgt aggctcattc atttctctaa cagcagtaat attaataatt ttcatgattt 7320 gagaagcctt cgcttcgaag cgaaaagtcc taatagtaga agaaccctcc ataaacctgg 7380 agtgactata tggatgcccc ccaccctacc acacattcga agaacccgta tacataaaat 7440 ctagacaaaa aaggaaggaa tcgaaccccc caaagctggt ttcaagccaa ccccatggcc 7500 tccatgactt tttcaaaaag gtattagaaa aaccatttca taactttgtc aaagttaaat 7560 tataggctaa atcctatata tcttaatggc acatgcagcg caagtaggtc tacaagacgc 7620 tacttcccct atcatagaag agcttatcac ctttcatgat cacgccctca taatcatttt 7680 ccttatctgc ttcctagtcc tgtatgccct tttcctaaca ctcacaacaa aactaactaa 7740 tactaacatc tcagacgctc aggaaataga aaccgtctga actatcctgc ccgccatcat 7800 cctagtcctc atcgccctcc catccctacg catcctttac ataacagacg aggtcaacga 7860 tccctccctt accatcaaat caattggcca ccaatggtac tgaacctacg agtacaccga 7920 ctacggcgga ctaatcttca actcctacat acttccccca ttattcctag aaccaggcga 7980 cctgcgactc cttgacgttg acaatcgagt agtactcccg attgaagccc ccattcgtat 8040 aataattaca tcacaagacg tcttgcactc atgagctgtc cccacattag gcttaaaaac 8100 agatgcaatt cccggacgtc taaaccaaac cactttcacc gctacacgac cgggggtata 8160 ctacggtcaa tgctctgaaa tctgtggagc aaaccacagt ttcatgccca tcgtcctaga 8220 attaattccc ctaaaaatct ttgaaatagg gcccgtattt accctatagc accccctcta 8280 ccccctctag agcccactgt aaagctaact tagcattaac cttttaagtt aaagattaag 8340 agaaccaaca cctctttaca gtgaaatgcc ccaactaaat actaccgtat ggcccaccat 8400 aattaccccc atactcctta cactattcct catcacccaa ctaaaaatat taaacacaaa 8460 ctaccaccta cctccctcac caaagcccat aaaaataaaa aattataaca aaccctgaga 8520 accaaaatga acgaaaatct gttcgcttca ttcattgccc ccacaatcct aggcctaccc 8580 gccgcagtac tgatcattct atttccccct ctattgatcc ccacctccaa atatctcatc 8640 aacaaccgac taatcaccac ccaacaatga ctaatcaaac taacctcaaa acaaatgata 8700 accatacaca acactaaagg acgaacctga tctcttatac tagtatcctt aatcattttt 8760 attgccacaa ctaacctcct cggactcctg cctcactcat ttacaccaac cacccaacta 8820 tctataaacc tagccatggc catcccctta tgagcgggca cagtgattat aggctttcgc 8880 tctaagatta aaaatgccct agcccacttc ttaccacaag gcacacctac accccttatc 8940 cccatactag ttattatcga aaccatcagc ctactcattc aaccaatagc cctggccgta 9000 cgcctaaccg ctaacattac tgcaggccac ctactcatgc acctaattgg aagcgccacc 9060 ctagcaatat caaccattaa ccttccctct acacttatca tcttcacaat tctaattcta 9120 ctgactatcc tagaaatcgc tgtcgcctta atccaagcct acgttttcac acttctagta 9180 agcctctacc tgcacgacaa cacataatga cccaccaatc acatgcctat catatagtaa 9240 aacccagccc atgaccccta acaggggccc tctcagccct cctaatgacc tccggcctag 9300 ccatgtgatt tcacttccac tccataacgc tcctcatact aggcctacta accaacacac 9360 taaccatata ccaatgatgg cgcgatgtaa cacgagaaag cacataccaa ggccaccaca 9420 caccacctgt ccaaaaaggc cttcgatacg ggataatcct atttattacc tcagaagttt 9480 ttttcttcgc aggatttttc tgagcctttt accactccag cctagcccct accccccaat 9540 taggagggca ctggccccca acaggcatca ccccgctaaa tcccctagaa gtcccactcc 9600 taaacacatc cgtattactc gcatcaggag tatcaatcac ctgagctcac catagtctaa 9660 tagaaaacaa ccgaaaccaa ataattcaag cactgcttat tacaatttta ctgggtctct 9720 attttaccct cctacaagcc tcagagtact tcgagtctcc cttcaccatt tccgacggca 9780 tctacggctc aacatttttt gtagccacag gcttccacgg acttcacgtc attattggct 9840 caactttcct cactatctgc ttcatccgcc aactaatatt tcactttaca tccaaacatc 9900 actttggctt cgaagccgcc gcctgatact ggcattttgt agatgtggtt tgactatttc 9960 tgtatgtctc catctattga tgagggtctt actcttttag tataaatagt accgttaact 10020 tccaattaac tagttttgac aacattcaaa aaagagtaat aaacttcgcc ttaattttaa 10080 taatcaacac cctcctagcc ttactactaa taattattac attttgacta ccacaactca 10140 acggctacat agaaaaatcc accccttacg agtgcggctt cgaccctata tcccccgccc 10200 gcgtcccttt ctccataaaa ttcttcttag tagctattac cttcttatta tttgatctag 10260 aaattgccct ccttttaccc ctaccatgag ccctacaaac aactaacctg ccactaatag 10320 ttatgtcatc cctcttatta atcatcatcc tagccctaag tctggcctat gagtgactac 10380 aaaaaggatt agactgaacc gaattggtat atagtttaaa caaaacgaat gatttcgact 10440 cattaaatta tgataatcat atttaccaaa tgcccctcat ttacataaat attatactag 10500 catttaccat ctcacttcta ggaatactag tatatcgctc acacctcata tcctccctac 10560 tatgcctaga aggaataata ctatcgctgt tcattatagc tactctcata accctcaaca 10620 cccactccct cttagccaat attgtgccta ttgccatact agtctttgcc gcctgcgaag 10680 cagcggtggg cctagcccta ctagtctcaa tctccaacac atatggccta gactacgtac 10740 ataacctaaa cctactccaa tgctaaaact aatcgtccca acaattatat tactaccact 10800 gacatgactt tccaaaaaac acataatttg aatcaacaca accacccaca gcctaattat 10860 tagcatcatc cctctactat tttttaacca aatcaacaac aacctattta gctgttcccc 10920 aaccttttcc tccgaccccc taacaacccc cctcctaata ctaactacct gactcctacc 10980 cctcacaatc atggcaagcc aacgccactt atccagtgaa ccactatcac gaaaaaaact 11040 ctacctctct atactaatct ccctacaaat ctccttaatt ataacattca cagccacaga 11100 actaatcata ttttatatct tcttcgaaac cacacttatc cccaccttgg ctatcatcac 11160 ccgatgaggc aaccagccag aacgcctgaa cgcaggcaca tacttcctat tctacaccct 11220 agtaggctcc cttcccctac tcatcgcact aatttacact cacaacaccc taggctcact 11280 aaacattcta ctactcactc tcactgccca agaactatca aactcctgag ccaataactt 11340 aatatgacta gcttacacaa tagcttttat agtaaagata cctctttacg gactccactt 11400 atgactccct aaagcccatg tcgaagcccc catcgctggg tcaatagtac ttgccgcagt 11460 actcttaaaa ctaggcggct atggtataat acgcctcaca ctcattctca accccctgac 11520 aaaacacata gcctacccct tccttgtact atccctatga ggcataatta taacaagctc 11580 catctgccta cgacaaacag acctaaaatc gctcattgca tactcttcaa tcagccacat 11640 agccctcgta gtaacagcca ttctcatcca aaccccctga agcttcaccg gcgcagtcat 11700 tctcataatc gcccacgggc ttacatcctc attactattc tgcctagcaa actcaaacta 11760 cgaacgcact cacagtcgca tcataatcct ctctcaagga cttcaaactc tactcccact 11820 aatagctttt tgatgacttc tagcaagcct cgctaacctc gccttacccc ccactattaa 11880 cctactggga gaactctctg tgctagtaac cacgttctcc tgatcaaata tcactctcct 11940 acttacagga ctcaacatac tagtcacagc cctatactcc ctctacatat ttaccacaac 12000 acaatggggc tcactcaccc accacattaa caacataaaa ccctcattca cacgagaaaa 12060 caccctcatg ttcatacacc tatcccccat tctcctccta tccctcaacc ccgacatcat 12120 taccgggttt tcctcttgta aatatagttt aaccaaaaca tcagattgtg aatctgacaa 12180 cagaggctta cgacccctta tttaccgaga aagctcacaa gaactgctaa ctcatgcccc 12240 catgtctaac aacatggctt tctcaacttt taaaggataa cagctatcca ttggtcttag 12300 gccccaaaaa ttttggtgca actccaaata aaagtaataa ccatgcacac tactataacc 12360 accctaaccc tgacttccct aattcccccc atccttacca ccctcgttaa ccctaacaaa 12420 aaaaactcat acccccatta tgtaaaatcc attgtcgcat ccacctttat tatcagtctc 12480 ttccccacaa caatattcat gtgcctagac caagaagtta ttatctcgaa ctgacactga 12540 gccacaaccc aaacaaccca gctctcccta agcttcaaac tagactactt ctccataata 12600 ttcatccctg tagcattgtt cgttacatgg tccatcatag aattctcact gtgatatata 12660 aactcagacc caaacattaa tcagttcttc aaatatctac tcatcttcct aattaccata 12720 ctaatcttag ttaccgctaa caacctattc caactgttca tcggctgaga gggcgtagga 12780 attatatcct tcttgctcat cagttgatga tacgcccgag cagatgccaa cacagcagcc 12840 attcaagcaa tcctatacaa ccgtatcggc gatatcggtt tcatcctcgc cttagcatga 12900 tttatcctac actccaactc atgagaccca caacaaatag cccttctaaa cgctaatcca 12960 agcctcaccc cactactagg cctcctccta gcagcagcag gcaaatcagc ccaattaggt 13020 ctccacccct gactcccctc agccatagaa ggccccaccc cagtctcagc cctactccac 13080 tcaagcacta tagttgtagc aggaatcttc ttactcatcc gcttccaccc cctagcagaa 13140 aatagcccac taatccaaac tctaacacta tgcttaggcg ctatcaccac tctgttcgca 13200 gcagtctgcg cccttacaca aaatgacatc aaaaaaatcg tagccttctc cacttcaagt 13260 caactaggac tcataatagt tacaatcggc atcaaccaac cacacctagc attcctgcac 13320 atctgtaccc acgccttctt caaagccata ctatttatgt gctccgggtc catcatccac 13380 aaccttaaca atgaacaaga tattcgaaaa ataggaggac tactcaaaac catacctctc 13440 acttcaacct ccctcaccat tggcagccta gcattagcag gaataccttt cctcacaggt 13500 ttctactcca aagaccacat catcgaaacc gcaaacatat catacacaaa cgcctgagcc 13560 ctatctatta ctctcatcgc tacctccctg acaagcgcct atagcactcg aataattctt 13620 ctcaccctaa caggtcaacc tcgcttcccc acccttacta acattaacga aaataacccc 13680 accctactaa accccattaa acgcctggca gccggaagcc tattcgcagg atttctcatt 13740 actaacaaca tttcccccgc atcccccttc caaacaacaa tccccctcta cctaaaactc 13800 acagccctcg ctgtcacttt cctaggactt ctaacagccc tagacctcaa ctacctaacc 13860 aacaaactta aaataaaatc cccactatgc acattttatt tctccaacat actcggattc 13920 taccctagca tcacacaccg cacaatcccc tatctaggcc ttcttacgag ccaaaacctg 13980 cccctactcc tcctagacct aacctgacta gaaaagctat tacctaaaac aatttcacag 14040 caccaaatct ccacctccat catcacctca acccaaaaag gcataattaa actttacttc 14100 ctctctttct tcttcccact catcctaacc ctactcctaa tcacataacc tattcccccg 14160 agcaatctca attacaatat atacaccaac aaacaatgtt caaccagtaa ctactactaa 14220 tcaacgccca taatcataca aagcccccgc accaatagga tcctcccgaa tcaaccctga 14280 cccctctcct tcataaatta ttcagcttcc tacactatta aagtttacca caaccaccac 14340 cccatcatac tctttcaccc acagcaccaa tcctacctcc atcgctaacc ccactaaaac 14400 actcaccaag acctcaaccc ctgaccccca tgcctcagga tactcctcaa tagccatcgc 14460 tgtagtatat ccaaagacaa ccatcattcc ccctaaataa attaaaaaaa ctattaaacc 14520 catataacct cccccaaaat tcagaataat aacacacccg accacaccgc taacaatcaa 14580 tactaaaccc ccataaatag gagaaggctt agaagaaaac cccacaaacc ccattactaa 14640 acccacactc aacagaaaca aagcatacat cattattctc gcacggacta caaccacgac 14700 caatgatatg aaaaaccatc gttgtatttc aactacaaga acaccaatga ccccaatacg 14760 caaaattaac cccctaataa aattaattaa ccactcattc atcgacctcc ccaccccatc 14820 caacatctcc gcatgatgaa acttcggctc actccttggc gcctgcctga tcctccaaat 14880 caccacagga ctattcctag ccatgcacta ctcaccagac gcctcaaccg ccttttcatc 14940 aatcgcccac atcactcgag acgtaaatta tggctgaatc atccgctacc ttcacgccaa 15000 tggcgcctca atattcttta tctgcctctt cctacacatc gggcgaggcc tatattacgg 15060 atcatttctc tactcagaaa cctgaaacat cggcattatc ctcctgcttg caactatagc 15120 aacagccttc ataggctatg tcctcccgtg aggccaaata tcattctgag gggccacagt 15180 aattacaaac ttactatccg ccatcccata cattgggaca gacctagttc aatgaatctg 15240 aggaggctac tcagtagaca gtcccaccct cacacgattc tttacctttc acttcatctt 15300 gcccttcatt attgcagccc tagcaacact ccacctccta ttcttgcacg aaacgggatc 15360 aaacaacccc ctaggaatca cctcccattc cgataaaatc accttccacc cttactacac 15420 aatcaaagac gccctcggct tacttctctt ccttctctcc ttaatgacat taacactatt 15480 ctcaccagac ctcctaggcg acccagacaa ttatacccta gccaacccct taaacacccc 15540 tccccacatc aagcccgaat gatatttcct attcgcctac acaattctcc gatccgtccc 15600 taacaaacta ggaggcgtcc ttgccctatt actatccatc ctcatcctag caataatccc 15660 catcctccat atatccaaac aacaaagcat aatatttcgc ccactaagcc aatcacttta 15720 ttgactccta gccgcagacc tcctcattct aacctgaatc ggaggacaac cagtaagcta 15780 cccttttacc atcattggac aagtagcatc cgtactatac ttcacaacaa tcctaatcct 15840 aataccaact atctccctaa ttgaaaacaa aatactcaaa tgggcctgtc cttgtagtat 15900 aaactaatac accagtcttg taaaccggag atgaaaacct ttttccaagg acaaatcaga 15960 gaaaaagtct ttaactccac cattagcacc caaagctaag attctaattt aaactattct 16020 ctgttctttc atggggaagc agatttgggt accacccaag tattgactca cccatcaaca 16080 accgctatgt atttcgtaca ttactgccag ccaccatgaa tattgtacgg taccataaat 16140 acttgaccac ctgtagtaca taaaaaccca atccacatca aaaccccctc cccatgctta 16200 caagcaagta cagcaatcaa ccctcaacta tcacacatca actgcaactc caaagccacc 16260 cctcacccac taggatacca acaaacctac ccacccttaa cagtacatag tacataaagc 16320 catttaccgt acatagcaca ttacagtcaa atcccttctc gtccccatgg atgacccccc 16380 tcagataggg gtcccttgac caccatcctc cgtgaaatca atatcccgca caagagtgct 16440 actctcctcg ctccgggccc ataacacttg ggggtagcta aagtgaactg tatccgacat 16500 ctggttccta cttcagggtc ataaagccta aatagcccac acgttcccct taaataagac 16560 atcacgatg 16569 

We claim:
 1. A method to aid in detecting the presence of tumor cells in a patient, comprising the steps of: determining the presence of a homoplasmic single basepair substitution in a mitochondrial genome of a cell sample of a patient, wherein the substitution is found in a tumor of the patient but not in normal tissue of the patient; and identifying the patient as having a tumor if one or more single basepair substitutions are determined in the mitochondrial genome of the cell sample of the patient.
 2. The method of claim 1 wherein, prior to the step of determining the presence of a single basepair substitution, the substitution has been identified in a tumor.
 3. The method of claim 1 wherein the cell sample is from a tissue suspected of harboring a metastasis.
 4. The method of claim 1 wherein the cell sample is from blood.
 5. The method of claim 1 wherein the cell sample is from urine.
 6. The method of claim 1 wherein the cell sample is from sputum.
 7. The method of claim 1 wherein the cell sample is from saliva.
 8. The method of claim 1 wherein the cell sample is from feces.
 9. The method of claim 1 wherein the step of determining comprises amplifying mitochondrial DNA.
 10. The method of claim 1 wherein the step of determining comprises sequencing mitochondrial DNA.
 11. The method of claim 1 wherein the step of determining comprises hybridization of DNA amplified from the mitochondrial genome of the cell sample to an array of oligonucleotides which comprises matched and mismatched sequences to human mitochondrial genomic DNA.
 12. The method of claim 2 wherein the substitution was identified previously in a tumor of the patient.
 13. The method of claim 12 wherein the patient has received anti-cancer therapy and the step of determining is performed at least three times to monitor progress of the anti-cancer therapy.
 14. The method of claim 1 further comprising the step of testing a normal tissue of the patient to determine the absence of the substitution in the normal tissue.
 15. The method of claim 1 wherein the cell sample is from a tumor.
 16. The method of claim 1 wherein the substitution is a T to a C mutation.
 17. The method of claim 1 wherein the substitution is a G to an A mutation.
 18. A method to aid in detecting the presence of tumor cells in a patient, comprising the steps of: determining the presence of a single basepair mutation in a mitochondrial genome of a cell sample of a patient, wherein the mutation is found in a tumor of the patient but not in normal tissue of the patient, and wherein the mutation has previously been identified as a somatic mutation in a tumor, and identifying the patient as having a tumor if one or more single basepair mutations are determined in the mitochondrial genome of the cell sample of the patient.
 19. The method of claim 18 wherein the cell sample is from a tissue suspected of harboring a metastasis.
 20. The method of claim 18 wherein the cell sample is from blood.
 21. The method of claim 18 wherein the cell sample is from urine.
 22. The method of claim 18 wherein the cell sample is from sputum.
 23. The method of claim 18 wherein the cell sample is from saliva.
 24. The method of claim 18 wherein the cell sample is from feces.
 25. The method of claim 18 wherein the step of determining comprises amplifying mitochondrial DNA.
 26. The method of claim 18 wherein the step of determining comprises sequencing mitochondrial DNA.
 27. The method of claim 18 wherein the step of determining comprises hybridization of DNA amplified from the mitochondrial genome of the cell sample to an array of oligonucleotides which comprises matched and mismatched sequences to human mitochondrial genomic DNA.
 28. The method of claim 18 wherein the single basepair mutation is a substitution mutation.
 29. The method of claim 18 wherein the single basepair mutation is a one basepair insertion.
 30. The method of claim 18 wherein the single basepair mutation is a one basepair deletion.
 31. The method of claim 18 wherein the single basepair mutation is a transition mutation.
 32. The method of claim 18 wherein the single basepair mutation is a homoplasmic mutation.
 33. The method of claim 18 wherein the mutation has previously been identified as a somatic mutation in a tumor of the patient.
 34. The method of claim 33 wherein the patient has received anti-cancer therapy and the step of determining is performed at least three times to monitor progress of the anti-cancer therapy.
 35. The method of claim 18 further comprising the step of testing a normal tissue of the patient to determine the absence of the mutation in the normal tissue.
 36. The method of claim 18 wherein the cell sample is from a tumor. 